Alignments for a candidate for fruK in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruK in Collimonas pratensis Ter91

Align Fructose import ATP-binding protein FruK; EC 7.5.2.- (characterized)
to candidate WP_061941304.1 CPter91_RS14020 sugar ABC transporter ATP-binding protein

Query= SwissProt::Q8G847
         (513 letters)



>NCBI__GCF_001584185.1:WP_061941304.1
          Length = 519

 Score =  469 bits (1208), Expect = e-137
 Identities = 244/500 (48%), Positives = 342/500 (68%), Gaps = 4/500 (0%)

Query: 6   PIVVMKGITIEFPGVKALDGVDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIM 65
           P + + GI   F GV AL+ V L LYPGEVH LMG+NGAGKST+IK LTGVY  ++G I+
Sbjct: 18  PALTLSGICKAFGGVTALNEVALRLYPGEVHTLMGQNGAGKSTLIKVLTGVYTPDSGRIL 77

Query: 66  VDGKPQQFNGTLDAQNAGIATVYQEVNLCTNLSVGENVMLGHEKRGPFGIDWKKTHEAAK 125
           + G+P Q   TL+AQ+ GI+TVYQEVNLC NLSV EN+ +G   +    IDWK   + A+
Sbjct: 78  LHGQPVQPRSTLEAQSLGISTVYQEVNLCPNLSVAENIFIGRYPKKYGAIDWKSMQQQAQ 137

Query: 126 KYLAQMGLESIDPHTPLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFA 185
           + L ++ +  ID   PLS   +A+QQ+VAI+RA+ I+AKVLILDEPTSSLD  EV+ LF 
Sbjct: 138 QLLHELHVR-IDVAAPLSRYPLAIQQMVAISRALSISAKVLILDEPTSSLDDAEVKLLFE 196

Query: 186 IMRKVRDSGVAILFVSHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           ++RK+R  G+AILFV+HFL+Q YEI+DR+T+LRNGQ   E +     R +L+  M+G   
Sbjct: 197 VLRKLRAQGMAILFVTHFLEQTYEISDRITVLRNGQLEGEYLASQLSRLDLVNKMVGSQT 256

Query: 246 AELSQIGAKKARRE--ITPGEKPIVDVKGLGKKGTINPVDVDIYKGEVVGFAGLLGSGRT 303
           +    + A   R E  +  G+  ++  +GLG+ G + P+D+D+  GEV+G  GLLGSGRT
Sbjct: 257 SSSPNLDAADGRAEPQVDSGQTAVLQARGLGRNGILAPLDLDLRGGEVLGLCGLLGSGRT 316

Query: 304 ELGRLLYGADKPDSGTYTLNGKKVNISDPYTALKNKIAYSTENRRDEGIIGDLTVRQNIL 363
           E  RLL+GADKPDSGT  + GK      P  A+   I + +E+R+ EG I +L+VR+NI+
Sbjct: 317 ETARLLFGADKPDSGTLQIKGKVEKFHSPRDAIAAGIGFCSEDRKKEGAILELSVRENIV 376

Query: 364 IALQATRGMFKPIPKKEADAIVDKYMKELNVRPADPDRPVKNLSGGNQQKVLIGRWLATH 423
           +ALQA  G+ + IP++   A+   Y+K L ++ AD + P+ +LSGGNQQK L+ RWLAT 
Sbjct: 377 LALQARAGLLRVIPRRRQQALASDYVKWLGIKTADIETPIGSLSGGNQQKALLARWLATD 436

Query: 424 PELLILDEPTRGIDIGAKAEIQQVVLDLASQGMGVVFISSELEEVVRLSDDIEVLKDRHK 483
           P +LILDEPTRGID+ AK EI + V+ L  +GM ++FISSE+ EV+R+SD + VL+DR  
Sbjct: 437 PAMLILDEPTRGIDVRAKQEIMEHVIALCRKGMAILFISSEISEVLRVSDRMLVLRDRKA 496

Query: 484 IAEIENDDTVSQATIVETIA 503
             E    + + + ++++ IA
Sbjct: 497 CGEYLRGE-LDEDSVLQVIA 515



 Score =  103 bits (257), Expect = 2e-26
 Identities = 64/225 (28%), Positives = 119/225 (52%), Gaps = 5/225 (2%)

Query: 26  VDLTLYPGEVHALMGENGAGKSTMIKALTGVYKINAGSIMVDGKPQQFNGTLDAQNAGIA 85
           +DL L  GEV  L G  G+G++   + L G  K ++G++ + GK ++F+   DA  AGI 
Sbjct: 295 LDLDLRGGEVLGLCGLLGSGRTETARLLFGADKPDSGTLQIKGKVEKFHSPRDAIAAGIG 354

Query: 86  TVYQE---VNLCTNLSVGENVMLGHEKRGPF--GIDWKKTHEAAKKYLAQMGLESIDPHT 140
              ++         LSV EN++L  + R      I  ++    A  Y+  +G+++ D  T
Sbjct: 355 FCSEDRKKEGAILELSVRENIVLALQARAGLLRVIPRRRQQALASDYVKWLGIKTADIET 414

Query: 141 PLSSISIAMQQLVAIARAMVINAKVLILDEPTSSLDANEVRDLFAIMRKVRDSGVAILFV 200
           P+ S+S   QQ   +AR +  +  +LILDEPT  +D    +++   +  +   G+AILF+
Sbjct: 415 PIGSLSGGNQQKALLARWLATDPAMLILDEPTRGIDVRAKQEIMEHVIALCRKGMAILFI 474

Query: 201 SHFLDQIYEITDRLTILRNGQFIKEVMTKDTPRDELIGMMIGKSA 245
           S  + ++  ++DR+ +LR+ +   E +  +   D ++ ++ G+ A
Sbjct: 475 SSEISEVLRVSDRMLVLRDRKACGEYLRGELDEDSVLQVIAGEGA 519


Lambda     K      H
   0.316    0.135    0.376 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 657
Number of extensions: 27
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 513
Length of database: 519
Length adjustment: 35
Effective length of query: 478
Effective length of database: 484
Effective search space:   231352
Effective search space used:   231352
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources